Recognition of Higher Order Patterns in Proteins: Immunologic Kernels

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Bremel, Robert D ^a   Homan, E Jane ^a  

^a IoGenetics LLC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATHEPSIN; EPITOPE; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; TETANUS TOXIN;

ARTICLE; B LYMPHOCYTE; BINDING AFFINITY; BINDING SITE; DNA FLANKING REGION; HUMAN; IMMUNOLOGICAL PROCEDURES; MAJOR HISTOCOMPATIBILITY COMPLEX; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

B-LYMPHOCYTES; CATHEPSINS; CLUSTER ANALYSIS; EPITOPES; EPITOPES, B-LYMPHOCYTE; HISTOCOMPATIBILITY ANTIGENS CLASS I; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; MODELS, IMMUNOLOGICAL; PEPTIDES; PROTEIN BINDING; PROTEINS; PROTEOLYSIS; TETANUS TOXIN;

EID: 84880768956     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070115     Document Type: Article

References (53)

1. Lanzavecchia A, (1985) Antigen-specific interaction between T and B cells. Nature 314: 537-539.
2. Davidson HW, Watts C, (1989) Epitope-directed processing of specific antigen by B lymphocytes. J Cell Biol 109: 85-92.
3. Bergtold A, Desai DD, Gavhane A, Clynes R, (2005) Cell surface recycling of internalized antigen permits dendritic cell priming of B cells. Immunity 23: 503-514.
4. Delamarre L, Pack M, Chang H, Mellman I, Trombetta ES, (2005) Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate. Science 307: 1630-1634.
5. Chatterjee B, Smed-Sorensen A, Cohn L, Chalouni C, Vandlen R, et al. (2012) Internalization and endosomal degradation of receptor-bound antigens regulate the efficiency of cross presentation by human dendritic cells. Blood.
6. Rock KL, Farfan-Arribas DJ, Shen L, (2010) Proteases in MHC class I presentation and cross-presentation. J Immunol 184: 9-15.
7. Shedlock DJ, Shen H, (2003) Requirement for CD4 T cell help in generating functional CD8 T cell memory. Science 300: 337-339.
8. McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L, (2012) Molecular programming of B cell memory. Nat Rev Immunol 12: 24-34.
9. Biro A, Herincs Z, Fellinger E, Szilagyi L, Barad Z, et al. (2003) Characterization of a trypsin-like serine protease of activated B cells mediating the cleavage of surface proteins. Biochim Biophys Acta 1624: 60-69.
10. Catron DM, Pape KA, Fife BT, van Rooijen N, Jenkins MK, (2010) A protease-dependent mechanism for initiating T-dependent B cell responses to large particulate antigens. J Immunol 184: 3609-3617.
11. Moss CX, Tree TI, Watts C, (2007) Reconstruction of a pathway of antigen processing and class II MHC peptide capture. EMBO J 26: 2137-2147.
12. Watts C, (2012) The endosome-lysosome pathway and information generation in the immune system. Biochim Biophys Acta 1824: 14-21.
13. Vijayakrishnan L, Sarkar S, Roy RP, Rao KV, (1997) B cell responses to a peptide epitope: IV. Subtle sequence changes in flanking residues modulate immunogenicity. J Immunol 159: 1809-1819.
14. Aiba Y, Kometani K, Hamadate M, Moriyama S, Sakaue-Sawano A, et al. (2010) Preferential localization of IgG memory B cells adjacent to contracted germinal centers. Proc Natl Acad Sci U S A 107: 12192-12197.
15. Sette A, Moutaftsi M, Moyron-Quiroz J, McCausland MM, Davies DH, et al. (2008) Selective CD4+T cell help for antibody responses to a large viral pathogen: deterministic linkage of specificities. Immunity 28: 847-858.
16. Barnett BC, Graham CM, Burt DS, Skehel JJ, Thomas DB, (1989) The immune response of BALB/c mice to influenza hemagglutinin: commonality of the B cell and T cell repertoires and their relevance to antigenic drift. EurJImmunol 19: 515-521.
17. Takeshita T, Takahashi H, Kozlowski S, Ahlers JD, Pendleton CD, et al. (1995) Molecular analysis of the same HIV peptide functionally binding to both a class I and a class II MHC molecule. J Immunol 154: 1973-1986.
18. Paul S, Piontkivska H, (2010) Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designs. BMC Microbiol 10: 212.
19. Vaughan K, Blythe M, Greenbaum J, Zhang Q, Peters B, et al. (2009) Meta-analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine-related issues. Parasite Immunol 31: 78-97.
20. Nakamura Y, Kameoka M, Tobiume M, Kaya M, Ohki K, et al. (1997) A chain section containing epitopes for cytotoxic T, B and helper T cells within a highly conserved region found in the human immunodeficiency virus type 1 Gag protein. Vaccine 15: 489-496.
21. Bremel RD, Homan EJ, (2010) An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches. Immunome Res 6: 7.
22. Bremel RD, Homan EJ, (2010) An integrated approach to epitope analysis II: A system for proteomic-scale prediction of immunological characteristics. Immunome Res 6: 8.
23. Homan EJ, Bremel RD, (2011) Patterns of predicted T-cell epitopes associated with antigenic drift in influenza H3N2 hemagglutinin. PLoS One 6: e26711.
24. Impens F, Colaert N, Helsens K, Ghesquiere B, Timmerman E, et al. (2010) A quantitative proteomics design for systematic identification of protease cleavage events. MolCell Proteomics 9: 2327-2333.
25. Biniossek ML, Nagler DK, Becker-Pauly C, Schilling O, (2011) Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S. JProteomeRes. 10: 5363-5373.
26. Honey K, Rudensky AY, (2003) Lysosomal cysteine proteases regulate antigen presentation. Nat Rev Immunol 3: 472-482.
27. BenMohamed L, Krishnan R, Longmate J, Auge C, Low L, et al. (2000) Induction of CTL response by a minimal epitope vaccine in HLA A*0201/DR1 transgenic mice: dependence on HLA class II restricted T(H) response. Hum Immunol 61: 764-779.
28. Andersen-Beckh B, Binz T, Kurazono H, Mayer T, Eisel U, et al. (1989) Expression of tetanus toxin subfragments in vitro and characterization of epitopes. Infect Immun 57: 3498-3505.
29. Diethelm-Okita BM, Raju R, Okita DK, Conti-Fine BM, (1997) Epitope repertoire of human CD4+T cells on tetanus toxin: identification of immunodominant sequence segments. J Infect Dis 175: 382-391.
30. Nakagawa TY, Rudensky AY, (1999) The role of lysosomal proteinases in MHC class II-mediated antigen processing and presentation. Immunol Rev 172: 121-129.
31. Villadangos JA, Bryant RA, Deussing J, Driessen C, Lennon-Dumenil AM, et al. (1999) Proteases involved in MHC class II antigen presentation. Immunol Rev 172: 109-120.
32. Costantino CM, Ploegh HL, Hafler DA, (2009) Cathepsin S regulates class II MHC processing in human CD4+HLA-DR+T cells. J Immunol 183: 945-952.
33. Bania J, Gatti E, Lelouard H, David A, Cappello F, et al. (2003) Human cathepsin S, but not cathepsin L, degrades efficiently MHC class II-associated invariant chain in nonprofessional APCs. Proc Natl Acad Sci U S A 100: 6664-6669.
34. Beers C, Honey K, Fink S, Forbush K, Rudensky A, (2003) Differential regulation of cathepsin S and cathepsin L in interferon gamma-treated macrophages. J Exp Med 197: 169-179.
35. Schechter I, Berger A, (1967) On the size of the active site in proteases. I. Papain. BiochemBiophysResCommun 27: 157-162.
36. Beck H, Schwarz G, Schroter CJ, Deeg M, Baier D, et al. (2001) Cathepsin S and an asparagine-specific endoprotease dominate the proteolytic processing of human myelin basic protein in vitro. EurJImmunol 31: 3726-3736.
37. Turk V, Stoka V, Vasiljeva O, Renko M, Sun T, et al. (2012) Cysteine cathepsins: from structure, function and regulation to new frontiers. BiochimBiophysActa 1824: 68-88.
38. Nielsen M, Lundegaard C, Lund O, Kesmir C, (2005) The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57: 33-41.
39. Larsen JE, Lund O, Nielsen M, (2006) Improved method for predicting linear B-cell epitopes. ImmunomeRes 2: 2.
40. Parker JM, Guo D, Hodges RS, (1986) New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25: 5425-5432.
41. Simitsek PD, Campbell DG, Lanzavecchia A, Fairweather N, Watts C, (1995) Modulation of antigen processing by bound antibodies can boost or suppress class II major histocompatibility complex presentation of different T cell determinants. J Exp Med 181: 1957-1963.
42. Batista FD, Iber D, Neuberger MS, (2001) B cells acquire antigen from target cells after synapse formation. Nature 411: 489-494.
43. Slansky JE, Jordan KR (2010) The Goldilocks model for TCR-too much attraction might not be best for vaccine design. PLoS Biol 8.
44. Storm van's Gravesande K, Layne MD, Ye Q, Le L, Baron RM, et al. (2002) IFN regulatory factor-1 regulates IFN-gamma-dependent cathepsin S expression. J Immunol 168: 4488-4494.
45. Landry SJ, (1997) Local protein instability predictive of helper T-cell epitopes. Immunol Today 18: 527-532.
46. Melton SJ, Landry SJ, (2008) Three dimensional structure directs T-cell epitope dominance associated with allergy. Clin Mol Allergy 6: 9.
47. Van Regenmortel MH, (2009) What is a B-cell epitope? Methods MolBiol 524: 3-20.
48. Rock KL, York IA, Saric T, Goldberg AL, (2002) Protein degradation and the generation of MHC class I-presented peptides. Adv Immunol 80: 1-70.
49. Bryant PW, Lennon-Dumenil AM, Fiebiger E, Lagaudriere-Gesbert C, Ploegh HL, (2002) Proteolysis and antigen presentation by MHC class II molecules. Adv Immunol 80: 71-114.
50. Merkin J, Russell C, Chen P, Burge CB, (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338: 1593-1599.
51. Johnson NL, (1949) Systems of frequency curves generated by methods of translation. Biometrika 36: 149-176.
52. Ward JH, (1963) Hierarchical Grouping to Optimize an Objective Function. JAmStatAssoc 48: 236-244.
53. Bloomfield P (2000) Fourier Analysis of Time Series: An Introduction. New York, NY: John Wiley and Sons, Inc.